Hi,

I had same problem since we do not install software in the system directory. I 
had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know 
if anyone has better solution.

Zhibin Lu
Bioinformatics Support

Ontario Institute for Cancer Research            
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
 
www.oicr.on.ca

> Date: Fri, 18 Feb 2011 13:17:26 -0500
> From: n...@bx.psu.edu
> To: golha...@umdnj.edu
> CC: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] cluster path question
> 
> Ryan Golhar wrote:
> > 
> > >Ryan Golhar wrote:
> > >>I'm setting up Galaxy to run on my cluster using drmaa.  I can see
> > >>jobs getting submitted to Torque however the jobs keep failing,
> > >>because the tools are in the default system path.
> > >>
> > >>How do I tell galaxy to append a directory to the path used by jobs?
> > >
> > >Hi Ryan,
> > >
> > >Whatever user is running the jobs will need to modify the $PATH in its
> > >shell startup files.  If you're using bash, this would probably be
> > >~/.bash_profile
> > 
> > It already is in .bashrc (which is called by .bash_profile) for the
> > galaxy user.  I can submit the script from the shell and it runs
> > okay so something is up with either how the galaxy app is submitting
> > the job or the environment being used by the galaxy job.
> 
> When you say submit via the shell, do you mean with qsub, or by logging
> in to a node and running the wrapper script?
> 
> I haven't tested Torque with the drmaa runner so perhaps it's submitting
> in a way which starts the shell in non-interactive, non-login mode.  Let
> me know if you can determine for certain that no shell startup files are
> being read, and I'll try to replicate this in my environment.
> 
> > I'd like to modify the job script to print out some debugging
> > information to determine what environment variables are set when the
> > job gets executed.  Actually, this would be a useful "tool" within
> > Galaxy to test the cluster.
> 
> That's probably the simplest method, to just create a tool that outputs
> (either to stdout or the output file) what you'd like to see.
> 
> > 
> 
> > begin:vcard
> > fn:Ryan Golhar, Ph.D.
> > n:Golhar;Ryan
> > org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics
> > adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA
> > email;internet:golha...@umdnj.edu
> > title:NGS Bioinformatics Specialist
> > tel;work:(732) 235-6613
> > tel;fax:(732) 235-6267
> > tel;cell:(732) 236-1176
> > x-mozilla-html:FALSE
> > url:http://www.cinj.org
> > version:2.1
> > end:vcard
> > 
> 
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